I've suddenly got a rhythmic sound when I pedal, sounds like rubbing or grinding. No sound when I coast. It takes a couple minutes when I first get on the bike for the sound to manifest. Happens on the flats when spinning in all gears. Bike is only 3 months old (Bike Friday NWT, Velocity rims and hubs, Sugino cranks).

Things i've done:
regreased both pedals
lubed chain (squirt lube)
reseated front and rear wheel in dropouts
checked tightness of crank bolts
retightened both seat mast and stem mast
checked brake pad clearance

The only wear I see is on the inside of the chain guard - where the chain rubs when on the smallest cog; the chainline in that position isn't perfect. If I know what it is I am sure I can fix it, but I have a really hard time figuring out where noises are coming from. Any ideas on what else to check would be most helpful; otherwise I'll head over to the shop.

Edited to add: I did lay the bike down on the non-drive side in a little fall not long before the noise started. Other than some scratches to quick releases I did not see any visible damage. I don't know if it's related.